SmartPhos
This is the development version of SmartPhos; for the stable release version, see SmartPhos.
A phosphoproteomics data analysis package with an interactive ShinyApp
Bioconductor version: Development (3.23)
To facilitate and streamline phosphoproteomics data analysis, we developed SmartPhos, an R package for the pre-processing, quality control, and exploratory analysis of phosphoproteomics data generated by MaxQuant and Spectronaut. The package can be used either through the R command line or through an interactive ShinyApp called SmartPhos Explorer. The package contains methods such as normalization and normalization correction, transformation, imputation, batch effect correction, PCA, heatmap, differential expression, time-series clustering, gene set enrichment analysis, and kinase activity inference.
Author: Shubham Agrawal [aut, cre]
, Junyan Lu [aut]
Maintainer: Shubham Agrawal <shubhamagrawal2706 at gmail.com>
citation("SmartPhos")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SmartPhos")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | BatchEffect, Clustering, DifferentialExpression, GUI, GeneExpression, GeneSetEnrichment, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, ShinyApps, Software, Visualization |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 4.4.0) |
| Imports | MultiAssayExperiment, SummarizedExperiment, data.table, shiny, shinythemes, shinyjs, shinyBS, shinyWidgets, parallel, DT, tools, stats, ggplot2, plotly, ggbeeswarm, pheatmap, grid, XML, MsCoreUtils, imputeLCMD, missForest, limma, proDA, decoupleR, piano, BiocParallel, doParallel, doRNG, e1071, magrittr, matrixStats, rlang, stringr, tibble, dplyr, tidyr, Biobase, vsn, factoextra, cowplot |
| System Requirements | |
| URL | https://lu-group-ukhd.github.io/SmartPhos/ |
| Bug Reports | https://github.com/Bioconductor/SmartPhos/issues |
See More
| Suggests | knitr, BiocStyle, PhosR, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SmartPhos |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SmartPhos |
| Package Short Url | https://bioconductor.org/packages/SmartPhos/ |
| Package Downloads Report | Download Stats |